DOCSLIB.ORG

The Structure of DNA in the Nucleosome Core

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Structure of DNA in the Nucleosome Core articles The structure of DNA in the nucleosome core Timothy J. Richmond & Curt A. Davey ETH Zu¨rich, Institut fu¨r Molekularbiologie und Biophysik, ETH-Ho¨nggerberg, CH-8093 Zu¨rich The authors contributed equally to this work ........................................................................................................................................................................................................................... The 1.9-A˚ -resolution crystal structure of the nucleosome core particle containing 147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented accuracy. The DNA structure is remarkably different from that in oligonucleotides and non- histone protein–DNA complexes. The DNA base-pair-step geometry has, overall, twice the curvature necessary to accommodate the DNA superhelical path in the nucleosome. DNA segments bent into the minor groove are either kinked or alternately shifted. The unusual DNA conformational parameters induced by the binding of histone protein have implications for sequence-dependent protein recognition and nucleosome positioning and mobility. Comparison of the 147-base-pair structure with two 146-base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling. DNA in eukaryotic cells is packaged repetitively into nucleosomes mobility15. Their mechanism of action most probably derives from by means of extensive association with histone proteins1–3. The the innate ability of nucleosomes to ‘slide’ along DNA without hierarchical chromatin structure formed is the genomic substrate releasing it3. relevant to the vital processes of DNA replication, recombination, An accurate, atomic-level description of DNA conformation in transcription, repair and chromosome segregation, and to the the nucleosome core and comparison with naked DNA is essential pathological progression of cancer and viral disease. Although to an understanding of chromatin properties such as those resulting nucleosomal organization of DNA is essentially ubiquitous from nucleosome position and mobility. Previously, the probable throughout genomes and generally repressive to gene expression, sequence-dependent features of nucleosomal DNA were proposed it also contributes to gene transcription in a gene-specific manner, by extrapolation from high-resolution DNA oligonucleotide struc- suggesting that nucleosome positioning in gene promoter regions is tures16. Here, a direct analysis of nucleosome DNA is made, important for genuine gene regulation in vivo4–6. The question permitted by the high quality of the DNA structure in the 1.9-A˚ - therefore arises of how chromatin structure, in which DNA is resolution X-ray structure of the nucleosome core particle normally highly compacted, permits site-specific access to regula- (NCP147)17,18, comparable to high-resolution oligonucleotide tory factors and more extensive exposure to the transcription structures. The persistently tight curvature of nucleosome core apparatus. DNA causes it to take on conformations not obviously present in The answer is likely to require a knowledge of DNA conformation oligonucleotides but about which there has been speculation for in the nucleosome core. The core comprises 147 base pairs (bp) of many years19. Furthermore, comparison of the DNA twist values DNA and the histone octamer; compared with the nucleosome, it measured for the 147-bp and 146-bp structures with the DNA lacks only 10–90 bp of linker DNA envisaged to be naked or bound sequence periodicity found in bulk chromatin indicates that the to histone H1. The histone-fold domains of the octamer organize DNA stretching observed in the nucleosome core is commonplace the central 129 of 147 bp in 1.59 left-handed superhelical turns with in vivo. a diameter only fourfold that of the double helix. The relatively straight 9-bp terminal segments contribute little to the curvature of Excess DNA curvature the complete 1.67-turn superhelix7. So far, the site-specific regulat- The ideal DNA superhelix that best fits the NCP147 DNA was ory factors that have been discovered bind the linker or terminal constructed from uniformly distributed base pairs by using B-form regions of the intact nucleosome. The lack of binding to the central DNA geometry. It has a radius of 41.9 A˚ and a pitch of 25.9 A˚ region of the superhelix might simply be a consequence of bending (Fig. 1a). Each base-pair step comprising two adjacent base pairs the double helix or, additionally, of unusual DNA conformations contributes 4.538 to the curvature of the ideal superhelix. However, induced by histone binding. At least one protein, HIV-1 integrase, the NCP147 superhelix is not bent uniformly owing to (1) the does prefer DNA bent around the nucleosome in contrast to naked anisotropic flexibility of DNA, (2) local structural features intrinsic DNA8. to the DNA sequence, and (3) irregularities dictated by the under- The initiation of DNA-dependent nuclear processes in the con- lying histone octamer. The NCP147 DNA is generally B-form as text of chromatin implies that nucleosome position is biased by the judged by the criterion of the phosphate ‘Z-coordinate’ with a value DNA sequence to facilitate access by initiation factors. Numerous of 20.18 ^ 0.69 A˚ (mean ^ s.d.; range 22.32 to 1.45 A˚ ). On the examples of positioned nucleosomes in gene promoter regions have basis of oligonucleotide structures, values falling in the range from been described both in vivo and in vitro9–11. Preferential positioning 21 to 0 are indicative of the B-form, whereas values above 2 signify could place factor-binding sequences in nucleosome linker or the A-form20. Other standard conformational parameters also terminal region DNA. Furthermore, nucleosomes are intrinsically indicate that the DNA is predominantly B-form (see Supplementary mobile and yield access to their DNA in vitro, allowing even RNA Table 1). polymerase to transcribe nucleosomal DNA without causing dis- Remarkably, the NCP147 DNA has double the base-pair-step sociation of the histone octamer12–14. In vivo, energy-dependent curvature necessary to produce the DNA superhelix path. The ideal chromatin remodelling factors, targeted by gene regulatory proteins superhelix fit to the NCP147 DNA yields 1.67 superhelical turns for and acting directly on the nucleosome core, augment nucleosome 133.6 bp (1.84 superhelical turns for 147 bp), bending the DNA NATURE | VOL 423 | 8 MAY 2003 | www.nature.com/nature © 2003 Nature Publishing Group 145 articles through 600.08, whereas the actual curvature of NCP147 DNA is for the ideal and actual curvatures, respectively, and thus the 1,333.38 (both scalar curvature values were calculated with the terminal regions do not account for the discrepancy. The excess is program Curves21). The use of only the central 129 bp to remove not adequately explained by the zigzag path of the NCP147 super- the effect of straightening of the superhelical path at the termini helix, as the overall root-mean-square deviation from the ideal path yields values of 579.38 and 1248.68 (9.75 ^ 5.138 per base-pair step) is only 1.42 A˚ (Fig. 1a). We find that the greater part of the excess curvature is a consequence of alternation of DNA form not revealed by criteria based on oligonucleotide structures. Determining the component of curvature directed towards superhelix formation exposes the origin of the form changes. The potential contributions to curvature from the roll and tilt (see Supplementary Fig. 1) of each base-pair step vary as sinusoidal functions of the accumulated twist angle (V) along the length of the double helix. To evaluate the actual contributions, the roll and tilt values for each base-pair step are multiplied by the corresponding cos V (CAT) and sin V (SAT), respectively. A convenient origin for the summation of V is taken as the central base pair located on the pseudo-two-fold symmetry axis of the particle (base pair 0 or dyad position). For the ideal superhelix, the CAT and SAT values multiplied by 4.538 yield the roll and tilt contributions to superhelix curvature at each base-pair step (iCATand iSAT; Fig. 1b). The actual roll and tilt values for NCP147 DNA are moderately well correlated with CAT (R ¼ 0.72, P , 0.0001) and SAT (R ¼ 0.54, P , 0.0001), respectively. The sum of roll and tilt multiplied by CAT and SAT, respectively, over all base-pair steps yields a curvature free of the effect of path deviations between the ideal and actual super- helices. The resulting value is 897.08, or 1.5-fold that required to accommodate the full NCP147 superhelix. Unlike the computer-generated ideal superhelix, for which cur- vature derives equally from roll and tilt (iCAT and iSAT; Fig. 1b), curvature for oligonucleotide and NCP147 DNA stems predomi- nately from the roll parameter. For DNA oligonucleotide structures, roll is favoured over tilt by 2:1 (ref. 22), presumably because it requires less base-pair unstacking for any particular bend angle. In the nucleosome core, this ratio is virtually identical at 1.9:1, but when the components that contribute to the superhelix only are considered, the ratio is 3.0:1. Curvature into the superhelix is therefore accumulated every approximately five base pairs, where either the major or minor groove faces the histone octamer. Never- theless, the NCP147 tilt component contributes 77% of that for the ideal superhelix (Fig. 1b; compare tilt and iSAT plots). In contrast, the roll component is 222% of the ideal contribution (Fig. 1b; compare roll and iCAT plots). Analyses of crystal structures of DNA oligonucleotides and protein–DNA complexes normally equate DNA bending with DNA curvature23 and rely on base-pair-step parameters to explain bending behaviour; for example, by using roll and tilt22,24, roll and twist16,25,26 or roll, tilt, twist, slide, shift and rise24,27. This type of approach is inadequate for nucleosome core DNA, given the substantial excess curvature that contributes to superhelix for- mation.
Load more

Recommended publications
  • H2A Ubiquitylated Mononucleosomes Next-Generation Substrates for Deubiquitylation Enzyme (DUB) Assays
    H2A Ubiquitylated Mononucleosomes Next-Generation Substrates for Deubiquitylation Enzyme (DUB) Assays Next-Generation DUB Assay Substrates are here. Get results that matter. • Enabling access to DUB targets that require nucleosome substrates in vitro • Proper substrates for DUB inhibitor development • Unmatched quality control for results you can trust Histone monoubiquitylation (ub1) acts as a critical signaling center that regulates cascades of downstream epigenetic enzymes to modify gene transcription. The physiological substrate for chromatin-targeting DUBs is the nucleosome (Nuc), the basic repeating unit of chromatin (comprised of histone proteins wrapped by DNA). Current high-throughput screening (HTS) DUB assays use unnatural modified or diubiquitin conjugates as substrates, which poorly mimic endogenous targets in vivo. In collaboration with Boston Biochem, EpiCypher is delivering ubiquitylated nucleosome substrates for drug screening and chromatin biology research. FIGURE 1 Ub Ub Schematic representation of mononucleosoms assembled from recombinant human histones Ub expressed in E. coli (two each of histones H2A, H2B, H3 and H4). H2A H2A Approximately 50% of the nucleosomes are monoubiquitylated on histone H2A lysine 118, while the other 50% are monoubiquitylated on both histone H2A lysine 118 and histone H2A lysine 119 (multi-mono- ubiquitylated). Next Generation Deubiquitylation Enzyme (DUB) Assay Substrates EpiCypher has developed recombinant mononucleosomes carrying monoubiquitylation on H2A. These ubiquitylated nucleosomes are generated enzymatically using the RING1B/BMI1 ubiquitin ligase complex. The resulting product is highly pure (>95% of nucleosomes are ubiquitylated) and consists of nucleosomes monoubiquitylated at H2A lysine 118/119 (Figure 1; the physiological target of RING1B/BMI1 in vivo). FIGURE 2 Deubiquitylation Assay Data: Mononucleosomes H2A Ubiquityl, Recombinant Human, Biotinylated (1 μg) were employed in a deubiquitylation (DUB) assay using no enzyme (Lane 1), USP5 (Lane 2) or USP16 (Lane 3) and run on an SDS PAGE gel.
    [Show full text]
  • FACT Is Recruited to the +1 Nucleosome of Transcribed Genes and Spreads in a Chd1-Dependent Manner
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.20.259960; this version posted August 21, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner Célia Jeronimo1, Andrew Angel2, Christian Poitras1, Pierre Collin1, Jane Mellor2 and François Robert1,3,4* 1 Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada. 2Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK. 3 Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard- Montpetit, Montréal, QC H3T 1J4, Canada. 4 Lead Contact *Correspondence: [email protected] The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models for how FACT finds its way to transcriptionally active chromatin include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails and binding partially disassembled nucleosomes. Here, we systematically tested these and other scenarios in Saccharomyces cerevisiae and found that FACT binds transcribed chromatin, not RNAPII. Through a combination of experimental and mathematical modeling evidence, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1.
    [Show full text]
  • Topography of the Histone Octamer Surface: Repeating Structural Motifs Utilized in the Docking of Nucleosomal
    Proc. Natl. Acad. Sci. USA Vol. 90, pp. 10489-10493, November 1993 Biochemistry Topography of the histone octamer surface: Repeating structural motifs utilized in the docking of nucleosomal DNA (histone fold/helix-strand-helix motif/parallel fi bridge/binary DNA binding sites/nucleosome) GINA ARENTS* AND EVANGELOS N. MOUDRIANAKIS*t *Department of Biology, The Johns Hopkins University, Baltimore, MD 21218; and tDepartment of Biology, University of Athens, Athens, Greece Communicated by Christian B. Anfinsen, August 5, 1993 ABSTRACT The histone octamer core of the nucleosome is interactions. The model offers strong predictive criteria for a protein superhelix offour spirally arrayed histone dimers. The structural and genetic biology. cylindrical face of this superhelix is marked by intradimer and interdimer pseudodyad axes, which derive from the nature ofthe METHODS histone fold. The histone fold appears as the result of a tandem, parallel duplication of the "helix-strand-helix" motif. This The determination of the structure of the histone octamer at motif, by its occurrence in the four dimers, gives rise torepetitive 3.1 A has been described (3). The overall shape and volume structural elements-i.e., the "parallel 13 bridges" and the of this tripartite structure is in agreement with the results of "paired ends of helix I" motifs. A preponderance of positive three independent studies based on differing methodolo- charges on the surface of the octamer appears as a left-handed gies-i.e., x-ray diffraction, neutron diffraction, and electron spiral situated at the expected path of the DNA. We have microscopic image reconstruction (4-6). Furthermore, the matched a subset of DNA pseudodyads with the octamer identification of the histone fold, a tertiary structure motif of pseudodyads and thus have built a model of the nucleosome.
    [Show full text]
  • Watanabe S, Resch M, Lilyestrom W, Clark N
    NIH Public Access Author Manuscript Biochim Biophys Acta. Author manuscript; available in PMC 2010 November 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Biochim Biophys Acta. 2010 ; 1799(5-6): 480±486. doi:10.1016/j.bbagrm.2010.01.009. Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Shinya Watanabe1,*, Michael Resch2,*, Wayne Lilyestrom2, Nicholas Clark2, Jeffrey C. Hansen2, Craig Peterson1, and Karolin Luger2,3 1 Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St.; Worcester, Massachusetts 01605 2 Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870 3 Howard Hughes Medical Institute Abstract The posttranslational modification of histones is a key mechanism for the modulation of DNA accessibility. Acetylated lysine 56 in histone H3 is associated with nucleosome assembly during replication and DNA repair, and is thus likely to predominate in regions of chromatin containing nucleosome free regions. Here we show by x-ray crystallography that mutation of H3 lysine 56 to glutamine (to mimic acetylation) or glutamate (to cause a charge reversal) has no detectable effects on the structure of the nucleosome. At the level of higher order chromatin structure, the K to Q substitution has no effect on the folding of model nucleosomal arrays in cis, regardless of the degree of nucleosome density. In contrast, defects in array-array interactions in trans (‘oligomerization’) are selectively observed for mutant H3 lysine 56 arrays that contain nucleosome free regions. Our data suggests that H3K56 acetylation is one of the molecular mechanisms employed to keep chromatin with nucleosome free regions accessible to the DNA replication and repair machinery.
    [Show full text]
  • DNA Condensation and Packaging
    DNA condensation and packaging October 13, 2009 Professor Wilma K. Olson Viral DNA - chain molecules in confined spaces Viruses come in all shapes and sizes Clockwise: Human immuno deficiency virus (HIV); Aeromonas virus 31, Influenza virus, Orf virus, Herpes simplex virus (HSV), Small pox virus Image from U Wisconsin Microbial World website: http://bioinfo.bact.wisc.edu DNA packaging pathway of T3 and T7 bacteriophages • In vivo pathway - solid arrows Fang et al. (2008) “Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.” J. Mol. Biol. 384, 1384-1399 Cryo EM images of T3 capsids with 10.6 kbp packaged DNA • Labels mark particles representative of different types of capsids • Arrows point to tails on capsids Fang et al. (2008) “Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.”” J. Mol. Biol. 384, 1384-1399 Cryo EM images of representative particles • (b) 10.6 kbp DNA • (c) 22 kbp DNA • (d) bacteriophage T3 Fang et al. (2008) “Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.” J. Mol. Biol. 384, 1384-1399 3D icosohedral reconstructions of cryo-EM-imaged particles Threefold surface views and central cross sections • (b) 10.6 kbp DNA • (c) 22 kbp DNA • (d) bacteriophage T3 Fang et al. (2008) “Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.” J. Mol. Biol. 384, 1384-1399 Top-down views of λ phage DNA toroids captured in cryo-EM micrographs Note the circumferential winding of DNA found in collapsed toroidal particles produced in the presence of multi-valent cations. Hud & Vilfan (2005) “Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size.” Ann.
    [Show full text]
  • Investigating the Epigenetic Mechanisms of Trophoblast Giant Cells
    Biology ︱ Assistant Professor Koji Hayakawa NUCLEOSOME STRUCTURE OF TROPHOBLAST GIANT CELL (TGC) Diploid TSC Polyploid TGC H2A H2B H2AX/ Investigating the H2AZ epigenetic mechanisms Entry into DNA Endocycle H3 H4 H3.3 of trophoblast giant cells TGCs possess a loose chromatin structure owing to alterations in the histone composition of the nucleosomes, which involves the replacement of canonical histones with histone variants such as H2AX, H2AZ, and H3.3 during differentiation. Trophoblast giant cells (TGCs) ucleosome is a large molecule in the placenta of rodents, are a unique days, and that certain histone variants Many polyploid cells identified in plants are found in the placental in the cell which is primarily cell type that replicate their DNA until were associated with differentiated walls of rodents and play a Nmade up of DNA and proteins. the cell contains thousands of copies, cells. Overall, there was much less and animals appear to have a secretory role in maintaining pregnancy. The major protein in nucleosome is unlike most cells which normally contain variation in TGCs compared to the In contrast to most cell types called a histone, around which DNA two sets of chromosomes (diploid cells). undifferentiated, diploid cells. They or nutritive function. which contain two copies of wraps. These proteins are classified into The reasons for this condition are not found the histone profile to be very from undifferentiated cells showed distinct concentrations of salt buffer to disrupt each chromosome (diploid), canonical histones and non-canonical clear. However, it has been suggested similar in differentiated TSCs at day six bands when digested, demonstrating that DNA-protein bonds.
    [Show full text]
  • Chapter 6 Protein Structure and Folding
    Chapter 6 Protein Structure and Folding 1. Secondary Structure 2. Tertiary Structure 3. Quaternary Structure and Symmetry 4. Protein Stability 5. Protein Folding Myoglobin Introduction 1. Proteins were long thought to be colloids of random structure 2. 1934, crystal of pepsin in X-ray beam produces discrete diffraction pattern -> atoms are ordered 3. 1958 first X-ray structure solved, sperm whale myoglobin, no structural regularity observed 4. Today, approx 50’000 structures solved => remarkable degree of structural regularity observed Hierarchy of Structural Layers 1. Primary structure: amino acid sequence 2. Secondary structure: local arrangement of peptide backbone 3. Tertiary structure: three dimensional arrangement of all atoms, peptide backbone and amino acid side chains 4. Quaternary structure: spatial arrangement of subunits 1) Secondary Structure A) The planar peptide group limits polypeptide conformations The peptide group ha a rigid, planar structure as a consequence of resonance interactions that give the peptide bond ~40% double bond character The trans peptide group The peptide group assumes the trans conformation 8 kJ/mol mire stable than cis Except Pro, followed by cis in 10% Torsion angles between peptide groups describe polypeptide chain conformations The backbone is a chain of planar peptide groups The conformation of the backbone can be described by the torsion angles (dihedral angles, rotation angles) around the Cα-N (Φ) and the Cα-C bond (Ψ) Defined as 180° when extended (as shown) + = clockwise, seen from Cα Not
    [Show full text]
  • Condensed DNA: Condensing the Concepts
    Progress in Biophysics and Molecular Biology 105 (2011) 208e222 Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio Review Condensed DNA: Condensing the concepts Vladimir B. Teif a,b,*, Klemen Bohinc c,d a BioQuant and German Cancer Research Center, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany b Institute of Bioorganic Chemistry, Belarus National Academy of Sciences, Kuprevich 5/2, 220141, Minsk, Belarus c Faculty of Health Sciences, Zdravstvena pot 5, 1000 Ljubljana, Slovenia d Faculty of Electrical Engineering, University of Ljubljana, Trzaska 25, 1000 Ljubljana, Slovenia article info abstract Article history: DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes Available online 16 July 2010 are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The Keywords: mechanistic details of DNA packing are essential for its functioning, as revealed by the recent devel- DNA condensation opments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Ligand binding Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in Counterion correlations the bulk of experimental and theoretical details. Here we try to condense some of these concepts and Macromolecular crowding fi Chromatin provide interconnections between the different elds. After a brief description of main experimental Gene regulation features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented.
    [Show full text]
  • And Beta-Helical Protein Motifs
    Soft Matter Mechanical Unfolding of Alpha- and Beta-helical Protein Motifs Journal: Soft Matter Manuscript ID SM-ART-10-2018-002046.R1 Article Type: Paper Date Submitted by the 28-Nov-2018 Author: Complete List of Authors: DeBenedictis, Elizabeth; Northwestern University Keten, Sinan; Northwestern University, Mechanical Engineering Page 1 of 10 Please doSoft not Matter adjust margins Soft Matter ARTICLE Mechanical Unfolding of Alpha- and Beta-helical Protein Motifs E. P. DeBenedictis and S. Keten* Received 24th September 2018, Alpha helices and beta sheets are the two most common secondary structure motifs in proteins. Beta-helical structures Accepted 00th January 20xx merge features of the two motifs, containing two or three beta-sheet faces connected by loops or turns in a single protein. Beta-helical structures form the basis of proteins with diverse mechanical functions such as bacterial adhesins, phage cell- DOI: 10.1039/x0xx00000x puncture devices, antifreeze proteins, and extracellular matrices. Alpha helices are commonly found in cellular and extracellular matrix components, whereas beta-helices such as curli fibrils are more common as bacterial and biofilm matrix www.rsc.org/ components. It is currently not known whether it may be advantageous to use one helical motif over the other for different structural and mechanical functions. To better understand the mechanical implications of using different helix motifs in networks, here we use Steered Molecular Dynamics (SMD) simulations to mechanically unfold multiple alpha- and beta- helical proteins at constant velocity at the single molecule scale. We focus on the energy dissipated during unfolding as a means of comparison between proteins and work normalized by protein characteristics (initial and final length, # H-bonds, # residues, etc.).
    [Show full text]
  • Effect of Superhelical Structure on the Secondary Structure of DNA Rings
    VOL. 5, PP. 691-696 (1967) Effect of Superhelical Structure on the Secondary Structure of DNA Rings DANIEL GLAUBIGER and JOHN E. HEARST, Departnient of Chemistry, University of California, Berkeley, California Synopsis A quantity, called the linking number, is defined, which specifies the total number of t,wists in a circular helix. The linking number is invariant under continuous deforma- tions of the ring and therefore enables one to calculate the influence of superhelical structures on the secondary helix of a circular molecule. The linking number can be determined by projecting the helix into a plane and counting strand crosses in the projection as described. For example, it has been shown that for each 180" twist in a left-handed superhelix, a right-handed 360" twist is removed from the secondary helix, thus allowing local unwinding. Introduction It is of interest to relate superhelical structure of helical molecules to their secondary structure.' By defining a quantity characteristic of two- stranded circular helical niolecules, related to the helical structure, and in- variant under continuous deformations of the molecule, we are able to evaluate the changes in helical structure brought about by the imposition of superhelical configurations on such molecules. The quantity of interest, called the linking number, is related to the number of turns/cycle for a circular helical molecule.* It will be shown that superhelical structures which are made from helical polymers con- tribute to this number and alter the contribution made by the secondary structure of the molecule to this number. This is made manifest as a change in the number of turns/cycle or as a change in the number of turns/ unit length.
    [Show full text]
  • Influence of the Sequence-Dependent Flexure of DNA on Transcription in E.Coli
    Volume 17 Number 22 1989 Nucleic Acids Research Influence of the sequence-dependent flexure of DNA on transcription in E.coli Christina M.Collis, Peter L.Molloy, Gerald W.Both and Horace R.Drew* CSIRO Division of Biotechnology, Laboratory for Molecular Biology, PO Box 184, North Ryde, NSW 2113, Australia Received August 11, 1989; Revised and Accepted October 20, 1989 ABSTRACT In order to study the effects of DNA structure on cellular processes such as transcription, we have made a series of plasmids that locate several different kinds of DNA structure (stiff, flexible or curved) near the sites of cleavage by commonly-used restriction enzymes. One can use these plasmids to place any DNA region of interest (e.g., promoter, operator or enhancer) close to certain kinds of DNA structure that may influence its ability to work in a living cell. In the present example, we have placed a promoter from T7 virus next to the special DNA structures; the T7 promoter is then linked to a gene for a marker protein (chloramphenicol acetyl transferase). When plasmids bearing the T7 promoter are grown in cells of E. coli that contain T7 RNA polymerase, the special DNA structures seem to have little or no influence over the activity of the T7 promoter, contrary to our expectations. Yet when the same plasmids are grown in cells of E. coli that do not contain T7 RNA polymerase, some of the DNA structures show a surprising promoter activity of their own. In particular, the favourable flexibility or curvature of DNA, in the close vicinity of potential -35 and -10 promoter regions, seems to be a significant factor in determining where E.
    [Show full text]
  • X-Ray Scattering from the Superhelix in Circular DNA (Supercoiling/Diffraction from Solutions/Specific Linking Difference/Writhe Vs
    Proc. Nati Acad. Sci. USA Vol. 80, pp. 741-744, February 1983 Biophysics X-ray scattering from the superhelix in circular DNA (supercoiling/diffraction from solutions/specific linking difference/writhe vs. twist) G. W. BRADY*, D. B. FEIN*, H. LAMBERTSONt, V. GRASSIANt, D. Foost, AND C. J. BENHAMt Institute, Troy, New York 12181; *Center for Laboratories and Research, New York State Department of Health, Albany, New York 12222; tRensselaer Polytechnic and tDepartment of Mathematics, University of Kentucky, Lexington, Kentucky 40506 Communicated by Bruno H. Zimm, October 25, 1982 ABSTRACT This communication presents measurements, creased the lower angle limit of resolution of the instrument made with a newly constructed position-sensitive detector, of the because the inner portion of the scattering curve was super- small-angle x-ray scattering from the first-order superhelix ofna- imposed on a risingbackground resultingfrom parasitic slit scat- tive COP608 plasmid DNA. This instrument measures intensities tering. In consequence, the resulting data could not be de- free of slit effects and provides good resolution in the region of smeared, so a direct comparison with theory was precluded. interest. The reported observations, made both in the presence This paper presents measurements of SAS from the first-or- and in the absence of intercalator, closely fit the scattering pat- der ccc DNA superhelix made with a new position-sensitive terns calculated for noninterwound helical first-order superhel- detector (PSD). The resulting profiles are free of slit effects, ices. These results are consistent with a toroidal helical structure permitting direct and unambiguous comparisons with theory. but not with interwound conformations.
    [Show full text]